|Thread||Thread Starter||Forum||Replies||Last Post|
|How to build reference genome for targeted region(from a BED file) for alignment?||serenaliao||Epigenetics||6||08-07-2015 01:44 PM|
|How to extract alignment of one reads mapped to specific region?||hujiacun||Bioinformatics||3||05-17-2015 11:32 PM|
|HLA region alignment||jbelmont||Bioinformatics||4||08-20-2012 03:57 PM|
|Alignment to selected region of the reference genome||houkto||General||1||02-20-2012 05:51 AM|
|alignment reads in homologous region||m_elena_bioinfo||Bioinformatics||7||03-16-2011 07:27 AM|
|04-19-2017, 10:58 AM||#1|
Join Date: Feb 2016
RNA-seq alignment on novel region
My colleagues just discovered a novel lncRNA region and I would like to check its expression in my 30 RNA-seq samples. The length of this region is 2438bp with two transcript variants, which are 645bp and 553bp (strand information is not available), respectively. I used STAR to perform the alignment on this region and bedtools multicov to count the expression on whole region and its two transcript variants. The procedure is shown below:
STAR --runMode genomeGenerate --genomeDir ./lncRNA-genome --genomeFastaFiles ./lncRNA.fa --genomeSAindexNbases 10 ####I extracted the sequences of this region and made fasta file and built up STAR index, since the length is small, so I have to change the "genomeSAindexNbases"
STAR --genomeDir ./lncRNA_genome --outSAMunmapped Within --runThreadN 4 --genomeLoad LoadAndRemove --limitBAMsortRAM 10000000002 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix sample1 --readFilesIn sample1.fastq ######STAR alignment only to this region
samtools index sample1.sorted.bam####index bam
bedtools multicov -bams sample1.sorted.bam -bed ./lncRNA.bed > results.txt#####bedtools to count expression on whole region and two variants
After counting the expression, I would like to use rpm (reads per million) to compare the expression for the whole region and two transcript variants among my 30 RNA-seq samples, respectively.
So I would like to know is there anything that I miss or have to pay attention to or you guys have some suggestions? Thanks!!
|alignment, count expression, star|